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- PDB-1bwx: THE SOLUTION STRUCTURE OF HUMAN PARATHYROID HORMONE FRAGMENT 1-39... -

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Entry
Database: PDB / ID: 1bwx
TitleTHE SOLUTION STRUCTURE OF HUMAN PARATHYROID HORMONE FRAGMENT 1-39, NMR, 10 STRUCTURES
ComponentsPARATHYROID HORMONE
KeywordsPEPTIDE HORMONE / SOLUTION STRUCTURE / HUMAN PARATHYROID HORMONE
Function / homology
Function and homology information


parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / macromolecule biosynthetic process / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis ...parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / macromolecule biosynthetic process / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis / positive regulation of signal transduction / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / response to vitamin D / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / Rho protein signal transduction / positive regulation of glycogen biosynthetic process / bone resorption / positive regulation of bone mineralization / response to cadmium ion / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / response to lead ion / hormone activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / response to ethanol / transcription by RNA polymerase II / G protein-coupled receptor signaling pathway / receptor ligand activity / response to xenobiotic stimulus / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsMarx, U.C. / Roesch, P. / Adermann, K. / Bayer, P. / Forssmann, W.-G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: Solution structures of human parathyroid hormone fragments hPTH(1-34) and hPTH(1-39) and bovine parathyroid hormone fragment bPTH(1-37).
Authors: Marx, U.C. / Adermann, K. / Bayer, P. / Forssmann, W.G. / Rosch, P.
History
DepositionSep 29, 1998Processing site: BNL
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PARATHYROID HORMONE


Theoretical massNumber of molelcules
Total (without water)4,5371
Polymers4,5371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Representative

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Components

#1: Protein/peptide PARATHYROID HORMONE


Mass: 4537.273 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01270

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: THE DISTANCE RESTRAINTS USED FOR STRUCTURE CALCULATION WERE OBTAINED FROM TWO-DIMENSIONAL HOMONUCLEAR 1H- NOESY SPECTRA.

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Sample preparation

DetailsContents: 10% D2O/90% H2O
Sample conditionsIonic strength: 320 mM / pH: 5.8 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE CALCULATION FOLLOWED STANDARD PROCEDURES EMPLOYING A HYBRID DISTANCE GEOMETRY MOLECULAR DYNAMICS APPROACH WITH SIMULATED ANNEALING REFINEMENT AND SUBSEQUENT ENERGY MINIMIZATION. ...Details: THE STRUCTURE CALCULATION FOLLOWED STANDARD PROCEDURES EMPLOYING A HYBRID DISTANCE GEOMETRY MOLECULAR DYNAMICS APPROACH WITH SIMULATED ANNEALING REFINEMENT AND SUBSEQUENT ENERGY MINIMIZATION. FOR THE REFINEMENT THE DIELECTRIC CONSTANT WAS CHANGED TO 4. STRUCTURE PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO AND TOPALLHDG.PRO OF X-PLOR 3.1. IN EACH ROUND OF THE STRUCTURE CALCULATION 30 STRUCTURES WERE CALCULATED. OF THE 30 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE CALCULATION, THOSE 10 STRUCTURES THAT SHOWED THE LOWEST TOTAL ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION.
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 30 / Conformers submitted total number: 10

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